I've done all of that<br>i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )<br><br><br>I've included this in the topology of the bilayer<br><br>; Include chain topologies<br>#include "gromos53a6_lipid.ff/forcefield.itp"<br>
#include "dppc.itp"<br><br>; Include water topology<br>#include "gromos53a6_lipid.ff/spc.itp"<br><br>; Include ion topologies<br>#include "gromos53a6_lipid.ff/ions.itp"<br><br>#ifdef POSRES_LIPID<br>
#include "posre_lipid.itp"<br>#endif<br><br>; System specifications<br>[ system ]<br>128-Lipid DMPC Bilayer in water<br><br>[ molecules ]<br>; molecule name nr.<br>DPPC 64<br>SOL 1193<br>SOL 690<br>
<br><br>Also I've tried to make posre for whole system ( large posres ) but it also was finished with same error<br><br>Fatal error:<br>[ file posre_lipid.itp, line 6 ]:<br>Atom index (2) in position_restraints out of bounds (1-1).<br>
This probably means that you have inserted topology section "position_restraints"<br>in a part belonging to a different molecule than you intended to.<br>In that case move the "position_restraints" section to the right molecule.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br><br>What's most true for such multy system. Generate posre only for 1 part or for whole system?<br>
<br>James<br><br><div class="gmail_quote">2011/10/31 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks, Justin<br>
I'll test your program soon.<br>
<br>
Today also I have some problems with generation of the posre for lipids<br>
<br>
I have lipid bilayer in pdb. Then I selected one lipid molecule and move it to separate pdb and convert it to gro via editconf.<br>
Than I've used genres and generate posre file for 1 lipid. Than I include tis posre to topology of my bilayer<br>
using gropt I obtain eror that I'm using wrong posre topology<br>
<br>
Also I've tried to include posre.itp to my lipid.itp ( this file contain link to posre on default) This run didnt produce any errors but as the result posres have not been worked ( I obtained perturbed bilayer after minimization)<br>
<br>
How I can generate work posre for my bilayer to prevent perturbation after equilibration or minimization ?<br>
<br>
</blockquote>
<br></div>
Since posre.itp is the default name given to the protein position restraint file by pdb2gmx, the first step is to use a different name. Then, you have to add the new #include statement in the correct location in the topology. Presuming you do that, the lipids should be restrained in whatever manner you've specified.<div>
<div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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